Design Of Ligands Research Articles

Recent Advances in Fluorescent Probes for G-quadruplex DNAs / RNAs.

Guanine-quadruplexes (G4s) are high-level structures formed by the folding of guaninerich nucleic acid sequences. G4s play important roles in various physiological processes, such as gene transcription, replication, recombination, and maintenance of chromosomal stability. Specific and sensitive monitoring of G4s lays the foundation for further understanding the structure, content, distribution, and function of G4s in organisms, which is important for the treatment and diagnosis of diseases. Moreover, visualization of G4s will provide new ideas for developing antitumor strategies targeting G4s. The design and development of G4-specific ligands are challenging due to the subtle differences in the structure of G4s. This review focuses on the progress of research on G4 fluorescent probes and their binding mechanisms to G4s. Finally, the challenges and future prospects for better detection and targeting of G4s in different organisms are discussed. This paper provides ideas for the development of novel G4 fluorescent probes.

Rationally Designed G-Quadruplex Selective "Turn-On" NIR Fluorescent Probe with Large Stokes Shift for Nucleic Acid Research-Based Applications.

Guanine-rich DNA/RNA sequences can form Hoogsteen bonds to adopt noncanonical secondary structures called G-quadruplexes, and these have been associated with diverse cellular processes. There has been considerable research interest in the design of G4-interacting ligands for cellular probing of the G4 structure and understanding its associated biological function. Most of the fluorescent G4 ligands either do not have significant selectivity over other nucleic acid structures, have high Stokes shift, or are not in the near-infrared (NIR) region, which limits its cellular visualization. The current work involves the rational design and synthesis of NIR fluorescent probes comprising a (Z)-1-methyl-2-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)quinolin-1-ium scaffold. Among the designed molecules, 4a exhibited far-red fluorescence (λmax = 680 nm) with large Stokes shift (∼182 nm) upon selective binding to human telomeric G-quadruplexes. The dye 4a does not disturb the conformation and stability of G-quadruplexes, thereby making it suitable for nucleic acid research based applications. Interestingly, 4a showed remarkable selectivity over single- and double-stranded structures in contrast to a commercially available quadruplex binding probe, Thiazole orange (TO). The molecular docking studies indicate that 4a binds at the groove region of the telomeric DNA G-quadruplex through π-π stacking interactions with the quinoline and amine-substituted phenyl ring and with the phosphate backbone through anion-π interactions with the benzothiazole ring. The designed molecule 4a has interesting photophysical properties, cell permeability, and biocompatibility with minimal cytotoxicity. Fluorescence imaging studies in live HeLa cells showed that probe 4a binds to the transient population of the DNA G-quadruplex in the nucleus and RNA quadruplexes in the cytoplasm. In brief, G-quadruplex NIR fluorescent probe 4a with a higher signal/noise ratio has significant potential for cellular imaging studies and thus opens avenues to decipher the biological pathways for better understanding of G-quadruplex biology.

Computer-Aided Identification and Design of Ligands for Multi-Targeting Inhibition of a Molecular Acute Myeloid Leukemia Network

Background/Objectives: Acute myeloid leukemia (AML) is characterized by therapeutic failure and long-term risk for disease relapses. As several therapeutic targets participate in networks, they can rewire to eventually evade single-target drugs. Hence, multi-targeting approaches are considered on the expectation that interference with many different components could synergistically hinder activation of alternative pathways and demolish the network one-off, leading to complete disease remission. Methods: Herein, we established a network-based, computer-aided approach for the rational design of drug combinations and de novo agents that interact with many AML network components simultaneously. Results: A reconstructed AML network guided the selection of suitable protein hubs and corresponding multi-targeting strategies. For proteins responsive to existing drugs, a greedy algorithm identified the minimum amount of compounds targeting the maximum number of hubs. We predicted permissible combinations of amiodarone, artenimol, fostamatinib, ponatinib, procaine, and vismodegib that interfere with 3–8 hubs, and we elucidated the pharmacological mode of action of procaine on DNMT3A. For proteins that do not respond to any approved drugs, namely cyclins A1, D2, and E1, we used structure-based de novo drug design to generate a novel triple-targeting compound of the chemical formula C15H15NO5, with favorable pharmacological and drug-like properties. Conclusions: Overall, by integrating network and structural pharmacology with molecular modeling, we determined two complementary strategies with the potential to annihilate the AML network, one in the form of repurposable drug combinations and the other as a de novo synthesized triple-targeting agent. These target–drug interactions could be prioritized for preclinical and clinical testing toward precision medicine for AML.

Stereochemical influence of 4ʹ-methyl substitutions on truncated 4ʹ-thioadenosine derivatives: Impact on A3 adenosine receptor binding and antagonism

Herein, we investigated the stereochemical effects of 4ʹ-methyl substitution on A3 adenosine receptor (A3AR) ligands by synthesizing and evaluating a series of truncated 4ʹ-thioadenosine derivatives featuring 4ʹ-α-methyl, 4ʹ-β-methyl, and 4ʹ,4ʹ-dimethyl substitutions. We successfully synthesized these derivatives, using the stereoselective addition of an organometallic reagent, KSAc-mediated sulfur cyclization, and Vorbrüggen condensation. Binding assays demonstrated that the 4ʹ-β-methyl substitution conferred the highest affinity for A3AR, with compound 1 h exhibiting a Ki = 3.5 nM, followed by the 4ʹ,4ʹ-dimethyl and 4ʹ-α-methyl substitutions. Notably, despite the absence of the 5ʹ-OH group, compound 1 h unexpectedly displayed partial agonism. Computational docking studies indicated that compound 1 h, the β-methyl derivative, adopted a South conformation and maintained strong interactions within the receptor, including a critical interaction with Thr94, a residue known to be notable for agonistic effects. Conversely, compound 2 h, the α-methyl derivative, also adopted a South conformation but resulted in a flattened structure that hindered interactions with Thr94 and Asn250. The dimethyl derivative 3 h exhibited steric clashes with Thr94, contributing to a reduction in binding affinity. However, the docking results for 3 h indicated a North conformation, suggesting that the change in sugar conformation due to the additional 4ʹ-methyl group altered the angle between the α-methyl group and the sugar plane, enabling binding despite the increased steric bulk. These findings suggest that not only do the substituents and their stereochemistry influence receptor–ligand interactions, but the conformation and the resulting spatial orientation of the substituents also play a crucial role in modulating receptor–ligand interaction. This stereochemical insight offers a valuable framework for the design of new, selective, and potent A3AR ligands, potentially facilitating the development of novel therapeutics for A3AR-related diseases such as glaucoma, inflammation, and cancer.

Gold‐Catalyzed Heck and Suzuki‐Type Reactions: Challenges and Recent Advances

AbstractTransition metal‐catalyzed Suzuki and Heck reactions are two of the most common carbon‐carbon bond formation reactions. Gold, unlike other transition metals (Pd, Ni, and Cu), offers unique reactivity profiles, and has emerged as an efficient tool in the field of synthetic organic chemistry. This mini‐review focused on the recent work in gold‐catalyzed Heck and Suzuki‐type reactions, especially by photocatalysts or ligand design, which show reactivities and features distinct from other transition metals. These discoveries will further facilitate the development of gold redox catalysis as well as applications in organic synthesis, biochemistry, and medicinal chemistry.

Mechanistic Studies of Small Molecule Ligands Selective to RNA Single G Bulges.

Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated Molecular Dynamics (GaMD) simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity-relationship (SAR) studies and transverse relaxation measurements by NMR spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Strikingly, small structure perturbations on these key contributors, such as the addition of a methyl group that disrupts the planarity of the ligand resulted in > 100-fold reduction in the binding affinity. Our work deepened the understanding of RNA-small molecule interactions and integrated a new generalizable platform for the rational design of selective small-molecule RNA binders.

Elucidating Polyphosphate Anion Binding to Lanthanide Complexes Using EXAFS and Pulsed EPR Spectroscopy.

Reversible anion binding to lanthanide complexes in aqueous solution has emerged as an effective method for anion sensing. Through careful design of the organic ligand, luminescent lanthanide complexes capable of binding biologically relevant anions in a bidentate or monodentate manner can be realized. While single-crystal X-ray diffraction analyses and NMR spectroscopy have revealed the structural geometry of several host-guest complexes, the challenge remains in designing preorganized lanthanide receptors with enhanced anion selectivity for broader applications in diagnostics and bioimaging. To address this challenge, innovative and complementary methods to investigate host-anion binding geometry are becoming increasingly important. Herein, we demonstrate the combined use of Eu L3-edge extended X-ray absorption fine structure (EXAFS) and electron paramagnetic resonance (EPR) spectroscopy to elucidate the binding of nucleoside phosphates (ATP, ADP, and AMP) to a cationic lanthanide complex. We establish that ATP unequivocally binds the lanthanide center in a bidentate manner in water, while ADP adopts both bidentate and monodentate modes, and AMP binds in a monodentate manner. This interdisciplinary approach provides deeper insight into lanthanide host-guest chemistry in solution, laying the groundwork for designing emissive probes that undergo specific anion-induced structural changes and elicit desired optical responses upon binding.

Conjugated Coordination Nanosheets with Molecular Rotors for Pseudocapacitors: Nanoarchitectonics and Enhanced Performance.

High-level pseudocapacitive materials require incorporations of significant redox regions into conductive and penetrable skeletons to enable the creation of devices capable of delivering high power for extended periods. Coordination nanosheets (CNs) are appealing materials for their high natural electrical conductivities, huge explicit surface regions, and semi-one-layered adjusted pore clusters. Thus, rational design of ligands and topological networks with desired electronic structure is required for the advancement in this field. Herein, we report three novel conjugated CNs (RV-10-M, M=Zn, Ni, and Co), by utilizing the full conjugation of the terpyridine-attached flexible tetraphenylethylene (TPE) units as the molecular rotors at the center. We prepare binder-free transparent nanosheets supported on Ni-foam with outstanding pseudocapacitive properties via a hydrothermal route followed by facile exfoliation. Among three CNs, the high surface area of RV-10-Co facilitates fast transport of ions and electrons and could achieve a high specific capacity of 670.8 C/g (1677 F/g) at 1 A/g current density. Besides, the corresponding flexible RV-10-Co possesses a maximum energy density of 37.26 Wh kg-1 at a power density of 171 W kg-1 and 70 % capacitance retention even after 1000 cycles.

Design and Synthesis of Small Molecule Probes of MDA-9/Syntenin

MDA-9/Syntenin, a key scaffolding protein and a molecular hub involved in a diverse range of cell signaling responses, has proved to be a challenging target for the design and discovery of small molecule probes. In this paper, we report on the design and synthesis of small molecule ligands of this key protein. Genetic algorithm-based computational design and the five–eight step synthesis of three molecules led to ligands with affinities in the range of 1–3 µM, a 20–60-fold improvement over literature reports. The design and synthesis strategies, coupled with the structure-dependent gain or loss in affinity, afford the deduction of principles that should guide the design of advanced probes of MDA-9/Syntenin.

Intrinsic Synergy and Selectivity for the Inhibition of Cancer Cell Growth Generated by a Polymer Ligand of Proximal Enzymes.

A fundamental understanding of the design of polymer ligands of proximal enzymes is essential for the precise targeting of cancer cells, but it is still in its infancy. In this study, we systematically investigated the contribution of the chain length, ligand density, and ligand ratio of proximal enzyme-targeted polymers to the efficacy, synergy, and selectivity for the inhibition of cancer cell proliferation. The results revealed that employing a moderate chain length as a scaffold allowed for an intrinsically high efficacy and synergy of proximal enzyme-targeted polymers, in contrast to single enzyme-targeted polymers that prefer longer chain length for efficacy. The synergy obtained in proximal enzyme targeting was not provided by the combination of the corresponding small molecules. Moreover, the maturation of the synergistic efficacy of the proximal enzyme-targeted polymers also improved selectivity. This study proposes a rational design for polymer inhibitors and/or ligands for cancer cells with a high efficacy and selectivity.

Enzymatic and Bio-Inspired Enantioselective Oxidation of Non-Activated C(sp 3)–H Bonds

AbstractThe enantioselective oxidation of C–H bonds relies on two different approaches: the use of enzymes or bio-inspired transition metal catalysts. Both are powerful tools, as they transform ubiquitous C(sp3)–H bonds into valuable oxygenated building blocks. However, the reaction remains a challenge in synthetic chemistry, continuously demanding efficient catalytic systems to improve substrate scopes. Optimization of site- and enantioselectivities in bio-catalytic systems is underpinned by protein engineering, while ligand design and medium effects play crucial roles in bio-inspired synthetic complexes. In this Short Review, recent advances in the field are described, focusing on reactions that target strong, non-activated C–H bonds.1 Introduction1.1 Enantioselective Catalytic C–H Oxidation in Nature and Bio-Inspired Systems1.2 Biological C–H Oxidation Mechanism and Challenges for the Implementation of Chirality with Synthetic Catalysts1.3 Bio-Catalytic C–H Oxidation Systems: From Microorganism to Engineered Enzymes1.4 Mimicking Nature: The Bio-Inspired C–H Oxidation Approach1.5 Origin of Enantioselectivity2 Enantioselective C–H Oxidation of Non-Activated C–H Bonds2.1 Hydroxylation at Non-Activated C–H Bonds by Bio-Catalytic Systems2.2 Enantioselective C–H Lactonization with Enzymatic Systems2.3 Oxidation at Non-Activated C–H Bonds by Synthetic Catalysts2.4 Enantioselective Lactonization with Small-Molecule Catalysts3 Conclusions

Crosslinkable Ligands for High-Density Photo-Patterning of Perovskite Nanocrystals.

Perovskite nanocrystals (PNCs) are promising luminescent materials for electronic color displays due to their high luminescence efficiency, widely-tunable emission wavelengths, and narrow emission linewidth. Their application in emerging display technologiesnecessitates precise micron-scale patterningwhile maintaining good optical performance. Although photolithography is a well-established micro-patterning technique in the industry, conventional processes are incompatible with PNCs as the use of polar solvents can damage the ionic PNCs, causingsevere luminescence quenching. Here,we report the rational design and synthesis of a new bidentate photo-crosslinkable ligand for the direct photo-patterning of PNCs. Each ligand contains two photosensitive acrylate groups and two carboxylate groups, and is introduced to the PNCs via an entropy-driven ligand exchange process. In a close-packed thin film, the acrylate ligands photo-polymerize and crosslink under ultraviolet light, rendering the PNCs insoluble in developing solvents. A high-density crosslinked PNC film with an optical density of 1.1 is attained at 1.4µm thickness, surpassing industry requirements on the absorption coefficient. Micron-scale patterning is further demonstrated using direct laser writing, producing well-defined 20µm features. This study thus offers an effective and versatile approach for micro-patterning PNCs, and may also be broadly applicable to other nanomaterial systems.

Consolidated Curium Reprocessing Procedure Inspires Molecular Design for Sensitized Curium Circularly Polarized Luminescence.

Curium's stable redox chemistry and ability to emit strong metal-based luminescence make it uniquely suitable for spectroscopic studies among the actinide series. Targeted ligand and coordination compound design can support both fundamental electronic structure studies and industrial safeguards with the identification of unique spectroscopic signatures. However, limited availability, inherent radioactive hazards, and arduous purifications have long inhibited such investigations of this element. A consolidated reprocessing procedure for curium has been developed for the milligram scale. The recovery of not only standard legacy curium samples but also hazardous legacy perchlorate containing curium samples was achieved, culminating in column chromatography utilizing the extraction resin DGA (N,N,N',N'-tetra-2-ethylhexyldiglycolamide, branched). Surprisingly, controlled elution of the Cm band from the extraction resin was followed through bright pink luminescence triggered by an inexpensive hand-held UV-vis lamp (380-400 nm). This observation inspired the design of an enantiopure, C2-symmetrical ligand bearing a chiral (trans-1,2-diaminocyclohexane) backbone with achiral DGA moieties (N,N,N',N'-tetra-n-octylacetamide), that enabled rarely observed curium circularly polarized luminescence upon metal chelation. These combined achievements should unlock more luminescence and circularly polarized luminescence studies of curium, and enable the recovery of many curium and other trivalent actinide samples.

Synthesis and study of bistriazolyl-pyrazines as new ligands for An/Ln separations

Herein, we present new hydrophilic tridentate ligands, bistriazolyl pyrazines. Their design was inspired by structurally similar and promising bis-triazolyl-pyridines (PyTri) ligands as well as theoretically derived criteria for the design of tridentate ligands for An/Ln separations suggested by theoretical studies. These ligands have been synthesised, characterised and tested as possible extractants for An/Ln nuclear separations. In addition, UV and fluorescence studies, pKa determination, and crystallographic and theoretical studies have been performed to explain their observed behaviour. Although the results of the solvent extraction studies have shown that these ligands do not possess sufficient selectivity for the extraction of Am vs Eu in i-SANEX conditions, this study presents a valuable test of the criteria for the design of tridentate heterocyclic N-donor ligands for advanced nuclear separation as postulated by theoretical studies a decade ago. Our experimental observations and theoretical studies have found that these criteria might not be the best guidance for designing novel hydrophilic ligands for An/Ln separations in i-SANEX conditions.

Resolving the Structure of a Guanine Quadruplex in TMPRSS2 Messenger RNA by Circular Dichroism and Molecular Modeling.

The presence of a guanine quadruplex in the opening reading frame of the messenger RNA coding for the transmembrane serine protease 2 (TMPRSS2) may pave the way to original anticancer and host-oriented antiviral strategy. Indeed, TMPRSS2 in addition to being overexpressed in different cancer types, is also related to the infection of respiratory viruses, including SARS-CoV-2, by promoting the cellular and viral membrane fusion through its proteolytic activity. The design of selective ligands targeting TMPRSS2 messenger RNA requires a detailed knowledge, at atomic level, of its structure. Therefore, we have used an original experimental-computational protocol to predict the first resolved structure of the parallel guanine quadruplex secondary structure in the RNA of TMPRSS2, which shows a rigid core flanked by a flexible loop. This represents the first atomic scale structure of the guanine quadruplex structure present in TMPRSS2 messenger RNA.

Asymmetric Hydrogenation of Naphthalenes with Molybdenum Catalysts: Ligand Design Improves Chemoselectivity

Asymmetric Hydrogenation of Naphthalenes with Molybdenum Catalysts: Ligand Design Improves Chemoselectivity

Development of Group IV Metal Complexes Bearing Thioether-Amido Ligands with Enhanced High-Temperature Catalytic Performance toward Olefin Copolymerization.

The development of homogeneous metal catalysts with both high activity and exceptional thermal stability is crucial for the efficient synthesis of polyolefin elastomers (POEs) through solution-phase olefin polymerization. In this study, a series of Hf (Hf1-Hf5), Zr (Zr1), and Ti (Ti1) complexes featuring thioether-amido ligands were synthesized and carefully characterized using advanced techniques such as 1H and 13C NMR spectroscopy as well as single-crystal X-ray diffraction analysis for Hf4 and Hf5. The results revealed that the catalytic activity and 1-octene incorporation efficiency of these metal complexes followed the trend Hf > Zr > Ti, underscoring the significant impact of the metal center on catalytic performance. Furthermore, the choice of ligands was found to play a critical role in dictating the catalytic properties, with ligands bearing less steric hindrance on the sulfur atom proving to be more favorable for copolymerization reactions. Notably, the Hf complex Hf1, featuring a methyl group on the sulfur atom, displayed exceptional catalytic activity as high as 21,060 kg(polymer)·mol-1(Hf)·h-1 toward ethylene/1-octene copolymerization at 120 °C and produced POE with a high molecular weight (Mw = 6.3 × 104 g·mol-1), relatively narrow distribution (Đ = 2.4), and high incorporation of 1-octene (34.1 mol %). This study demonstrates the potential of tailored ligand design in developing efficient metal catalysts for the production of high-value-added POEs.

Selective ligand recognition and activation of somatostatin receptors SSTR1 and SSTR3

Somatostatin receptors (SSTRs) exert critical biological functions such as negatively regulating hormone release and cell proliferation, making them popular targets for developing therapeutics to treat endocrine disorders, especially neuroendocrine tumors. Although several panagonists mimicking the endogenous ligand somatostatin are available, the development of more effective and safer somatostatinergic therapies is limited due to a lack of molecular understanding of the ligand recognition and regulation of divergent SSTR subtypes. Here, we report four cryoelectron microscopy structures of Gi-coupled SSTR1 and SSTR3 activated by distinct agonists, including the FDA-approved panagonist pasireotide as well as their selective small molecule agonists L-797591 and L-796778. Our structures reveal a conserved recognition pattern of pasireotide in SSTRs attributed to the binding with a conserved extended binding pocket, distinct from SST14, octreotide, and lanreotide. Together with mutagenesis analyses, our structures further reveal the dynamic feature of ligand binding pockets in SSTR1 and SSTR3 to accommodate divergent agonists, the key determinants of ligand selectivity lying across the orthosteric pocket of different SSTR subtypes, as well as the molecular mechanism underlying diversity and conservation of receptor activation. Our work provides a framework for rational design of subtype-selective SSTR ligands and may facilitate drug development efforts targeting SSTRs with improved therapeutic efficacy and reduced side effects.

Theoretical design of new ligands to boost reaction rate and selectivity in palladium-catalyzed aromatic fluorination.

The development of palladium-catalyzed fluorination with biaryl monophosphine ligands has faced two important problems that limit its application for bromoarenes: the formation of regioisomers and insufficient catalysis for heteroaryl substrates as bromothiophene derivatives. Overcoming these problems requires more ligand design. In this work, reliable theoretical calculations were used to elucidate important ligand features necessary for achieving more rate acceleration and selectivity. These features include increasing the ligand-substrate repulsion and creating a negative charge in the space around the fluoride ion bonded to the palladium. The investigated L5 ligand presents these features, and the calculations predict that this ligand completely suppresses the regioisomer formation in the difficult case of 4-bromoanisole. In addition, the free energy barriers are decreased by 2-3 kcal mol-1 in comparison with the catalysis involving the AlPhos ligand. Thus, the present study points out a direction for new developments in palladium-catalyzed fluorination.

Nano-synthesis, characterization, theoretical, biological and catalytic studies of Mn(II), Cu(II), Cd(II), and Th(IV) complexes based on antipyrine azo dye ligand

The design and detailed characterization of the azo dye ligand obtained from the reaction of 4-aminoantipyrine diazonium salt with 3-hydroxybenzaldehyde (HL) and its novel metal chelates with Mn2+, Cu2+, Cd2+ and Th4+ ions have been presented. Utilizing modern spectroscopic and analytical techniques, these complexes were found to adopt an octahedral geometry, demonstrate inner sphere d2sp3 hybridization for Th(IV) complex and outer sphere sp3d2 hybridization for other complexes. Particle sizes calculated using the Debye-Scherrer equation on XRD patterns were 32.05 nm for Mn(II), 34.07 nm for Cu(II), 30.90 nm for Cd(II), and 22.05 nm for Th(IV). These substances' anticancer activity was assessed on human lung cancer cells (A-549) and pancreatic carcinoma cell lines (PANC-1). Cd(II) complex exhibited higher cytotoxicity against the A-549 cell line than the reference drug vinblastine sulfate which revealing its potential application as a new anticancer agent. Quantum chemical computations using the DMOL3 module's density functional theory (DFT) and molecular docking studies with the Schrödinger suite demonstrated significant inhibitory effects of the free organic compound and Cu(II) chelate on the FGFR1 protein, crucial for cell development and differentiation. Additionally, the study examined the catalytic activity of HL and its metal chelates in the oxidative degradation of methyl violet 2B dye in presence of H2O2. The order was followed by the pseudo-first-order rate constants: Th(IV) chelate (0.9556 min⁻¹) > HL (0.4911 min⁻¹) > Cu(II) chelate (0.5979 min⁻¹) > Mn(II) chelate (0.2645 min⁻¹) > Cd(II) chelate (0.2280 min⁻¹).